CONTENTS
The DOE knowledgebase (kBASE) was searched for genomes from six major phyla found in soil microbial communities. A total of 24,268 genomes were found to correspond to the six major phyla. Results were trimmed to eliminate duplicates within a given genus, resulting in 1,082 unique genera. These genera were searched in the primary literature to determine habitat preference, and eliminate non-soil bacterial species. Ultimately, 231 species were selected for analysis.
| Genomes | Genera | Selections | |
|---|---|---|---|
| Alpha | 1709 | 197 | 32 |
| Beta | 1092 | 114 | 30 |
| Gamma | 7731 | 240 | 19 |
| Delta | 185 | 56 | 10 |
| Actino | 4055 | 191 | 25 |
| Acido | 25 | 12 | 25 |
| Firm | 8668 | 233 | 25 |
| Verr | 36 | 9 | 36 |
| Plancto | 29 | 12 | 29 |
Note: most of the subsequent analyses currently include only Actino, Acido, Verr, Plancto and Betaproteobacteria.
## null device
## 1
A database of exchange reactions was built to represent the full range of metabolites possible for uptake across all models. Number of C atoms and Gibbs free energy were noted for each metabolite. Models were compared for similarity of exchange reaction identity using MDS ordination.
## Run 0 stress 0.193728
## Run 1 stress 0.1916959
## ... New best solution
## ... procrustes: rmse 0.01880379 max resid 0.1134417
## Run 2 stress 0.1930628
## Run 3 stress 0.2056006
## Run 4 stress 0.4148659
## Run 5 stress 0.2061946
## Run 6 stress 0.2167616
## Run 7 stress 0.1980802
## Run 8 stress 0.200008
## Run 9 stress 0.1963522
## Run 10 stress 0.1937525
## Run 11 stress 0.2312129
## Run 12 stress 0.1937272
## Run 13 stress 0.2125163
## Run 14 stress 0.1944729
## Run 15 stress 0.202756
## Run 16 stress 0.2215017
## Run 17 stress 0.2230842
## Run 18 stress 0.1951894
## Run 19 stress 0.2014534
## Run 20 stress 0.2007262
CUE=(Net C Uptake - Respiration)/(Total C Uptake)
Carbon use efficiency was explored under two scenarios. (1) Unconstrained CUE was calculated by allowing a model to utilize all exchange reactions present, and (2) Constrained CUE was calculated by limiting the availability of a single constraining C-containing metabolite while leaving all other unconstrained.
Unconstrained CUE ranged from 0.077259 to 0.916791. Average unconstained CUE was 0.5338781 +/- 0.1642163.
Unconstrained CUE was analyzed for a phylogenetic signal. K values of 1 correspond to a Brownian motion process, which implies some degree of phylogenetic signal or conservatism. K values closer to zero correspond to a random or convergent pattern of evolution, while K values greater than 1 indicate strong phylogenetic signal and conservatism of traits.
Unconstrained CUE was found to have a significant phylogenetic signal (K = 0.03, p<0.01).
The following heat maps show trait distribution across the phylogenetic tree. Exrxns = number of exchange reactions, Cexrxns = number of C-containing exchange reactions, CUE=unconstrained carbon use efficiency, GC=guanine-cytosine, Genes= number of genes, DNA size= number of base pairs.
| K | PIC.variance.obs | PIC.variance.rnd.mean | PIC.variance.P | PIC.variance.Z | |
|---|---|---|---|---|---|
| Exrxns | 0.1640496 | 2.051194e+03 | 3.681776e+04 | 0.001 | -2.5807560 |
| Cexrxns | 0.1725261 | 1.635154e+03 | 3.092815e+04 | 0.001 | -2.6985569 |
| CUE | 0.0377776 | 9.143651e-01 | 3.866792e+00 | 0.003 | -1.8840388 |
| GC | 1.2898714 | 7.349652e+01 | 1.006113e+04 | 0.001 | -2.7610550 |
| Contigs | 0.1758305 | 4.540426e+06 | 1.011696e+08 | 0.008 | -0.7268392 |
| Genes | 0.3146108 | 1.591306e+07 | 5.702364e+08 | 0.001 | -2.5990916 |
| DNAsize | 0.5020087 | 1.307122e+13 | 7.391281e+14 | 0.001 | -2.6955093 |
Phylogenetic Independent Contrasts were used to test for relationships between CUE and genome traits.
| Intercept | Slope | R-Adj | |
|---|---|---|---|
| Exrxns | 0.9608944 | -0.0039505 | 0.1457687 |
| Cexrxns | 0.8801619 | -0.0042273 | 0.1393639 |
| GC | 0.9156732 | -0.0063604 | 0.0995834 |
| Genes | 0.7608438 | -0.0000448 | 0.2943128 |
| DNAsize | 0.7659457 | 0.0000000 | 0.3229883 |
For each model in the unconstrained environment, C-containing exchange reactions were classified according to the following hierarchy:
- Essential: reactions that are required for biomass production, identified as reactions that result in no biomass production when availability is set to zero.
- Constraining: reactions that biomass production responds to the availability of, i.e. reactions needed at more than a low threshold.
The uptake kinetics of the most common constraining reactions across models were analyzed. The availability of constraining reactions was then set to the concentration resulting in (a) 1/2 and (b) 1/4 of maximum biomass and CUE was recalculated.
The uptake kinetics were compared for the most common constraining C-containing exchange reactions. Preliminarily, it appears that uptake kinetics for a given metabolite do not vary between models, but that different metabolite have different uptake kinetics. Biomass flux v. substrate-specific uptake was plotted for a single acidobacterial model and curves were fit with linear model and Michaelis-Menten (MM) models. Both fits were assessed at 50% max biomass and 25% max biomass, and the substrate concentrations at these values from the LM fits were used as uptake bounds for the constrained CUE calculations.
gly.phe.10K = the upper bound of all reactions was increased by one or order of magnitude. gly.phe.10K1K = upper bound of all intracellular reactions and biomass production set to one order of magnitude greater than exchange reactions.
Fitting LM and MM Models to Uptake Kinetics
| uptake | L.Lysine | Gly.Phe.1K | Gly.Phe.10K | Gly.Phe.10K1K | ocdca | TRHL | Gly.Tyr | ddca | gly.asn.L | L.Isoleucine | Myristic.acid | Ala.His | L.Phenylalanine | L.Arginine | L.Tyrosine | D.Arabinose | Cytidine | L.Valine | L.Proline | L.Histidine | Glycerol.3.phosphate | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Km | NA | 155.1838328 | 50.4380138 | 6.378709e+02 | 514.564269 | 30.9441102 | 58.63531 | 28.0279135 | 58.63531 | 103.470412 | 125.531434 | 75.7168209 | 27.6516428 | 78.5264815 | 99.88237 | 55.45183 | 25.5975707 | 128.4957229 | 173.4981942 | 102.244632 | 27.6516428 | 99.045680 |
| Vm | NA | 1097.0794735 | 1053.1013772 | 1.136925e+04 | 9876.940300 | 1047.5678450 | 1056.66670 | 1046.9682062 | 1056.66670 | 1079.640287 | 1087.261558 | 1065.2770580 | 1046.8203125 | 1066.7497918 | 1077.89557 | 1055.20884 | 1046.0672293 | 1088.3203816 | 1100.9812684 | 1078.429742 | 1046.8203125 | 1077.465721 |
| lm-intercept | NA | -0.0000267 | 0.0000045 | 1.444028e-01 | 12.425781 | -0.0000044 | 0.00000 | 0.0000044 | 0.00000 | 0.000014 | -0.000027 | -0.0000045 | -0.0000167 | 0.0000091 | 0.00000 | 0.00000 | -0.0000167 | 0.0000054 | -0.0000076 | 9.087836 | -0.0000167 | 0.000000 |
| lm-slope | NA | 3.2211451 | 8.7803970 | 8.779215e+00 | 8.695916 | 11.7392473 | 7.99661 | 12.4926327 | 7.99661 | 4.979316 | 4.135675 | 6.6638419 | 12.6161319 | 6.4716755 | 5.17069 | 8.28661 | 13.3276840 | 4.0328230 | 2.8390284 | 4.875667 | 12.6161319 | 5.217443 |
| uptake at 500 | NA | 155.2243107 | 56.9450328 | 5.693625e+01 | 56.069331 | 42.5921688 | 62.52650 | 40.0235890 | 62.52650 | 100.415406 | 120.899252 | 75.0317927 | 39.6318000 | 77.2597443 | 96.69889 | 60.33830 | 37.5158966 | 123.9826288 | 176.1165937 | 100.686157 | 39.6318000 | 95.832379 |
| uptake at 250 | NA | 77.6121595 | 28.4725162 | 2.845990e+01 | 27.320205 | 21.2960846 | 31.26325 | 20.0117943 | 31.26325 | 50.207701 | 60.449629 | 37.5158967 | 19.8159007 | 38.6298715 | 48.34945 | 30.16915 | 18.7579489 | 61.9913137 | 88.0582982 | 49.411121 | 19.8159007 | 47.916189 |
Constrained CUE was reduced relative to unconstrained CUE, but the effect size varied by metabolite. Plots show unconstrained CUE versus constrained CUE for most common constraining metabolite at 50% maximum biomass and at 25% maximum biomass.
CONSTRAINED/UNCONSTRAINED COMPARISONS AND COHENS D
| Cohens D | Paired T-test Pval | |
|---|---|---|
| his500 | 0.187 | 0.228 |
| cyt500 | 0.393 | 0.007 |
| pro500 | 0.104 | 0.331 |
| arg500 | 0.298 | 0.001 |
| phenyl500 | 0.324 | 0.033 |
| myristic500 | 0.302 | 0.001 |
| isoleucine500 | 0.412 | 0.000 |
| tyr500 | 0.461 | 0.005 |
| glyasn500 | 0.505 | 0.000 |
| alahis500 | 0.458 | 0.000 |
| ddca500 | 0.593 | 0.000 |
| trhl500 | 0.710 | 0.000 |
| g3p500 | 0.000 | 1.000 |
| ocdca500 | 0.793 | 0.000 |
| ara500 | 0.855 | 0.000 |
| glytyr500 | 0.809 | 0.000 |
| lys500 | 1.576 | 0.000 |
| glyphe500 | 1.330 | 0.000 |
| val250 | 0.164 | 0.117 |
| his250 | 0.211 | 0.174 |
| cyt250 | 0.534 | 0.000 |
| pro250 | 0.068 | 0.528 |
| arg250 | 0.335 | 0.000 |
| phenyl250 | 0.509 | 0.001 |
| myristic250 | 0.267 | 0.003 |
| isoleucine250 | 0.442 | 0.000 |
| tyr250 | 0.429 | 0.009 |
| glyasn250 | 0.536 | 0.000 |
| alahis250 | 0.526 | 0.000 |
| ddca250 | 0.672 | 0.000 |
| trhl250 | 0.894 | 0.000 |
| g3p250 | 0.000 | 0.997 |
| ocdca250 | 0.886 | 0.000 |
| ara250 | 1.176 | 0.000 |
| glytyr250 | 0.891 | 0.000 |
| lys250 | 1.875 | 0.000 |
| glyphe250 | 1.408 | 0.000 |